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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ), 'gf_id' => 'HOM05D001583', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001583' ), 'data_identifier' => 'HOM05D001583', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001583', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '405', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17720' => 'bna', 'A03p17800' => 'bna', 'A04p24170' => 'bna', 'A04p24190' => 'bna', 'A04p25540' => 'bna', 'A05p14050' => 'bna', 'A05p14090' => 'bna', 'Aa31LG4G16680' => 'aar', 'Aa31LG5G5340' => 'aar', 'Aa31LG5G5380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.609' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.218' => 'aag', 'Actinidia25696' => 'ach', 'Actinidia30203' => 'ach', 'Actinidia38468' => 'ach', 'Actinidia39672' => 'ach', 'Ah.09g231380' => 'amhyb', 'Ah.14g085100' => 'amhyb', 'AL4G26860' => 'aly', 'AL5G34850' => 'aly', 'AL7G44360' => 'aly', 'Aqoxy3G01737' => 'aox', 'Aqoxy410s002' => 'aox', 'Aqoxy4G01027' => 'aox', 'Aqoxy5G01758' => 'aox', 'Aqoxy7G01078' => 'aox', 'arahy.Tifrunner.gnm1.ann1.61AUMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BLU73S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3YBRW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TGSI8L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9IBQP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI949D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSY9GG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4YWGS' => 'arhy', 'AT2G31610' => 'ath', 'AT3G53870' => 'ath', 'AT5G35530' => 'ath', 'ATR0598G300' => 'atr', 'ATR0772G128' => 'atr', 'Atru.chr7.1672' => 'acertr', 'Atru.chr7.1860' => 'acertr', 'AUR62025183' => 'cqu', 'AUR62028991' => 'cqu', 'AUR62036282' => 'cqu', 'AUR62039731' => 'cqu', 'BcaB01g04030' => 'bca', 'BcaB01g04034' => 'bca', 'BcaB02g10399' => 'bca', 'BcaB02g10402' => 'bca', 'BcaB06g26244' => 'bca', 'BcaB06g28534' => 'bca', 'BcaC01g05938' => 'bca', 'BcaC01g05942' => 'bca', 'BcaC02g11261' => 'bca', 'BcaC02g11262' => 'bca', 'BcaC02g11266' => 'bca', 'BcaC03g16284' => 'bca', 'BcaC07g38454' => 'bca', 'BcaC08g43103' => 'bca', 'BcaC08g44423' => 'bca', 'BcaNung02335' => 'bca', 'BcaNung03871' => 'bca', 'BcaNung05016' => 'bca', 'BolC1t01260H' => 'bol', 'BolC2t09106H' => 'bol', 'BolC2t10097H' => 'bol', 'BolC3t14443H' => 'bol', 'BolC3t14468H' => 'bol', 'BolC4t23389H' => 'bol', 'BolC4t23393H' => 'bol', 'BolC4t27581H' => 'bol', 'BolC4t27583H' => 'bol', 'BolC6t35511H' => 'bol', 'BolC7t41770H' => 'bol', 'BolC8t48864H' => 'bol', 'BraA01t03866Z' => 'bra', 'BraA03t11036Z' => 'bra', 'BraA03t11045Z' => 'bra', 'BraA04t17937Z' => 'bra', 'BraA04t17939Z' => 'bra', 'BraA04t18058Z' => 'bra', 'BraA05t20330Z' => 'bra', 'BraA05t20336Z' => 'bra', 'C01p10340' => 'bna', 'C01p12840' => 'bna', 'C02p30560' => 'bna', 'C02p40800' => 'bna', 'C03p20800' => 'bna', 'C03p20880' => 'bna', 'C04p18290' => 'bna', 'C04p18370' => 'bna', 'C04p18420' => 'bna', 'C04p60900' => 'bna', 'C04p60910' => 'bna', 'C06p03730' => 'bna', 'C06p18610' => 'bna', 'C06p24690' => 'bna', 'C07p03050' => 'bna', 'C07p12850' => 'bna', 'C08p12240' => 'bna', 'CAN.G148.18' => 'can', 'CAN.G148.19' => 'can', 'CAN.G6.36' => 'can', 'CAN.G88.10' => 'can', 'CANSAT25G0432' => 'cansat', 'CANSAT56G1563' => 'cansat', 'CANSAT56G3468' => 'cansat', 'CARHR125190' => 'chi', 'CARHR125260' => 'chi', 'CARHR217570' => 'chi', 'Carub.0004s1291' => 'cru', 'Carub.0005s2045' => 'cru', 'Carub.0007s3128' => 'cru', 'Ca_11195_v3' => 'car', 'Ca_11901_v3' => 'car', 'Ca_30872_v3' => 'car', 'CBR_g5657' => 'cbr', 'Cc04_g01410' => 'ccan', 'Cc06_g11970' => 'ccan', 'CDE04G2182' => 'cde', 'CDE06G0799' => 'cde', 'CDE06G0866' => 'cde', 'CDE06G1145' => 'cde', 'CDE06G1984' => 'cde', 'CDE07G0924' => 'cde', 'CDE07G1431' => 'cde', 'Cfa003025' => 'cfa', 'Cfa018013' => 'cfa', 'Ciclev10009346m.g' => 'ccl', 'Ciclev10010430m.g' => 'ccl', 'Ciclev10026299m.g' => 'ccl', 'CiPaw.01G219700' => 'cil', 'CiPaw.03G209500' => 'cil', 'CiPaw.04G145300' => 'cil', 'CiPaw.16G070100' => 'cil', 'ClCG07G014020' => 'cla', 'ClCG09G000930' => 'cla', 'ClCG11G001510' => 'cla', 'COL.COLO4_04771' => 'col', 'COL.COLO4_18124' => 'col', 'COL.COLO4_18125' => 'col', 'COL.COLO4_21077' => 'col', 'COL.COLO4_21125' => 'col', 'Cpa.g.sc126.35' => 'cpa', 'Cpa.g.sc28.74' => 'cpa', 'Cre02.g102250' => 'cre', 'CsaV3_2G001240' => 'csa', 'CsaV3_7G034530' => 'csa', 'CSS0001906' => 'camsi', 'CSS0004897' => 'camsi', 'CSS0009807' => 'camsi', 'CSS0015705' => 'camsi', 'CSS0025170' => 'camsi', 'CSS0039483' => 'camsi', 'DCAR_024734' => 'dca', 'DCAR_028292' => 'dca', 'Dinv02780' => 'din', 'Dinv25575' => 'din', 'Dinv42373' => 'din', 'Duzib150G0707' => 'dzi', 'Duzib168G0430' => 'dzi', 'Duzib168G2159' => 'dzi', 'Duzib187G1388' => 'dzi', 'Duzib187G1442' => 'dzi', 'ECA246G0138' => 'eca', 'ECA246G1035' => 'eca', 'ECA246G2981' => 'eca', 'EL10Ac2g02678' => 'bvu', 'EL10Ac2g03795' => 'bvu', 'EL10Ac8g19114' => 'bvu', 'Eucgr.C00719' => 'egr', 'Eucgr.C00830' => 'egr', 'Eucgr.C03560' => 'egr', 'Eucgr.L02999' => 'egr', 'FAN06G1440' => 'fan', 'FAN06G2153' => 'fan', 'FAN14G3480' => 'fan', 'FAN19G2463' => 'fan', 'FAN20G1335' => 'fan', 'FAN23G0969' => 'fan', 'FAN24G0638' => 'fan', 'FAN26G1460' => 'fan', 'FAN26G1547' => 'fan', 'FAN27G3454' => 'fan', 'FAN28G0226' => 'fan', 'FvH4_1g08300' => 'fve', 'FvH4_2g31150' => 'fve', 'FvH4_6g45290' => 'fve', 'FvH4_7g29220' => 'fve', 'Glyma.09G156600' => 'gma', 'Glyma.10G133100' => 'gma', 'Glyma.10G133800' => 'gma', 'Glyma.16G207300' => 'gma', 'Glyma.16G207400' => 'gma', 'Glyma.20G083300' => 'gma', 'Gohir.A05G032866' => 'ghi', 'Gohir.A05G039200' => 'ghi', 'Gohir.A07G014300' => 'ghi', 'Gohir.A07G020350' => 'ghi', 'Gohir.D05G034300' => 'ghi', 'Gohir.D05G040700' => 'ghi', 'Gohir.D07G013900' => 'ghi', 'Gorai.001G014700' => 'gra', 'Gorai.001G020800' => 'gra', 'Gorai.009G034700' => 'gra', 'Gorai.009G041200' => 'gra', 'GSVIVG01009619001' => 'vvi', 'GSVIVG01015110001' => 'vvi', 'GSVIVG01016775001' => 'vvi', 'GSVIVG01027950001' => 'vvi', 'GSVIVG01035451001' => 'vvi', 'GSVIVG01037802001' => 'vvi', 'HanXRQChr04g0096621' => 'han', 'HanXRQChr06g0171911' => 'han', 'HanXRQChr11g0320621' => 'han', 'HanXRQChr15g0479091' => 'han', 'HanXRQChr15g0479101' => 'han', 'HanXRQChr17g0540741' => 'han', 'HanXRQChr17g0543641' => 'han', 'HanXRQChr17g0543661' => 'han', 'Haze_18116' => 'cav', 'Haze_25976' => 'cav', 'Haze_26111' => 'cav', 'Hma1.2p1_0169F.1_g074700' => 'hma', 'Hma1.2p1_0797F.1_g219470' => 'hma', 'Hma1.2p1_1018F.1_g248450' => 'hma', 'HPP92_004372' => 'vpl', 'HPP92_016197' => 'vpl', 'Hund03299' => 'sun', 'Hund08716' => 'sun', 'Hund19426' => 'sun', 'Lalb_Chr08g0232521' => 'lal', 'Lalb_Chr08g0232531' => 'lal', 'Lalb_Chr11g0074301' => 'lal', 'Lalb_Chr11g0074311' => 'lal', 'Lalb_Chr13g0299541' => 'lal', 'Lalb_Chr23g0276411' => 'lal', 'Lj1g0017929' => 'lja', 'Lj3g0003073' => 'lja', 'Lj6g0000652' => 'lja', 'Lj7A683T68' => 'lonja', 'Lj7A684T30' => 'lonja', 'Lsat_1_v5_gn_3_25961' => 'lsa', 'Lsat_1_v5_gn_3_32760' => 'lsa', 'Lsat_1_v5_gn_3_43920' => 'lsa', 'Lsat_1_v5_gn_3_43961' => 'lsa', 'Lsat_1_v5_gn_4_23840' => 'lsa', 'Manes.03G038800' => 'mes', 'Manes.03G052600' => 'mes', 'Manes.16G084800' => 'mes', 'Manes.16G097200' => 'mes', 'Mapoly0001s0014' => 'mpo', 'MBI13_g11358_MAGBIO' => 'mbi', 'MBI19_g11848_MAGBIO' => 'mbi', 'MCO14G195' => 'mco', 'MD02G1087300' => 'mdo', 'MD08G1070300' => 'mdo', 'MD09G1184600' => 'mdo', 'MD09G1184700' => 'mdo', 'MD10G1087800' => 'mdo', 'MD15G1051900' => 'mdo', 'MD15G1214900' => 'mdo', 'Medtr1g023000' => 'mtr', 'Medtr1g044660' => 'mtr', 'Medtr1g111450' => 'mtr', 'Medtr6g052140' => 'mtr', 'Medtr6g052220' => 'mtr', 'MELO3C004645.2' => 'cme', 'MELO3C024359.2' => 'cme', 'Migut.E01152' => 'egut', 'Migut.I01067' => 'egut', 'Migut.J00945' => 'egut', 'Migut.J00946' => 'egut', 'Migut.L01547' => 'egut', 'MSTRG.19473' => 'ama', 'MSTRG.26460' => 'ama', 'Nitab4.5_0000073g0080' => 'nta', 'Nitab4.5_0000446g0250' => 'nta', 'Nitab4.5_0001488g0120' => 'nta', 'Nitab4.5_0001866g0050' => 'nta', 'Nitab4.5_0006849g0010' => 'nta', 'Nn1g02059' => 'nnu', 'Nn3g21743' => 'nnu', 'Nn6g35597' => 'nnu', 'Nn7g37158' => 'nnu', 'Nn8g38707' => 'nnu', 'Oeu010817.1' => 'oeu', 'Oeu039771.1' => 'oeu', 'Oeu040370.1' => 'oeu', 'Oeu049525.1' => 'oeu', 'Oeu058723.1' => 'oeu', 'Os03g0577000' => 'osa', 'Os07g0608500' => 'osa', 'Peaxi162Scf00101g01521' => 'pax', 'Peaxi162Scf00240g00106' => 'pax', 'PGR031G0951' => 'pgr', 'PGR142G3603' => 'pgr', 'PGSC0003DMG400016939' => 'stu', 'PGSC0003DMG400019563' => 'stu', 'Phvul.004G131800' => 'pvu', 'Phvul.004G131900' => 'pvu', 'Phvul.007G231200' => 'pvu', 'Potri.006G222100' => 'ptr', 'Potri.012G076800' => 'ptr', 'Potri.015G071700' => 'ptr', 'Potri.018G049100' => 'ptr', 'Pp3c11_22640' => 'ppa', 'Pp3c15_21360' => 'ppa', 'Pp3c16_3760' => 'ppa', 'Pp3c27_1320' => 'ppa', 'Pp3c5_5330' => 'ppa', 'Pp3c7_2620' => 'ppa', 'Pp3c9_12170' => 'ppa', 'PRCOL_00005678' => 'pco', 'Prupe.1G405800' => 'ppe', 'Prupe.3G042800' => 'ppe', 'Prupe.7G202300' => 'ppe', 'Psat6g001760' => 'psa', 'Psat6g107000' => 'psa', 'Psat6g109360' => 'psa', 'Psat6g229840' => 'psa', 'PSO210G1009' => 'pso', 'PSO210G3788' => 'pso', 'PSO210G5910' => 'pso', 'PSO210G6307' => 'pso', 'QL02p000145' => 'qlo', 'QL02p061016' => 'qlo', 'QL05p008061' => 'qlo', 'QL05p008094' => 'qlo', 'QL05p008098' => 'qlo', 'RcHm_v2.0_Chr2g0094371' => 'rch', 'RcHm_v2.0_Chr2g0171721' => 'rch', 'RcHm_v2.0_Chr6g0276121' => 'rch', 'RcHm_v2.0_Chr6g0311621' => 'rch', 'Rhsim01G0152500' => 'rsi', 'Rhsim01G0252000' => 'rsi', 'Rhsim03G0229700' => 'rsi', 'Rhsim05G0012000' => 'rsi', 'Sabra06G0171800' => 'sbr', 'Sabra12G0055000' => 'sbr', 'Sabra15G0076300' => 'sbr', 'Sabra15G0096600' => 'sbr', 'Sabra18G0046700' => 'sbr', 'SalBow1G1002' => 'sbo', 'SalBow1G1749' => 'sbo', 'SalBow1G7310' => 'sbo', 'SalBow2G1687' => 'sbo', 'SalBow5G3674' => 'sbo', 'SalBow6G3673' => 'sbo', 'SalBow6G5725' => 'sbo', 'SalBow7G1258' => 'sbo', 'Sc08g0008790' => 'sci', 'Sc09g0010040' => 'sci', 'Sed0002712' => 'sed', 'Sed0023788' => 'sed', 'SEGI_04305' => 'sgi', 'SEGI_30130' => 'sgi', 'SGA_v2.0_scaffold122G33332' => 'sas', 'SGA_v2.0_scaffold21G09477' => 'sas', 'SGA_v2.0_scaffold513G52645' => 'sas', 'SGA_v2.0_scaffold71G23862' => 'sas', 'SHI12404' => 'shi', 'SMO340G0282' => 'smo', 'SMO356G0177' => 'smo', 'SMO356G0412' => 'smo', 'Solyc07g041310.3' => 'sly', 'Solyc08g061843.1' => 'sly', 'Solyc08g061955.1' => 'sly', 'Sopen07g020630' => 'spe', 'Sopen08g017410' => 'spe', 'Sopen08g017480' => 'spe', 'Sp4g14040' => 'spa', 'Sp7g06820' => 'spa', 'SpUn1065_0010' => 'spa', 'TAR624G0335' => 'tar', 'TAR625G1464' => 'tar', 'TAR626G0714' => 'tar', 'TAR636G2264' => 'tar', 'TAR636G2357' => 'tar', 'THA.LOC104808896' => 'tha', 'THA.LOC104811215' => 'tha', 'THA.LOC104815324' => 'tha', 'THA.LOC104826583' => 'tha', 'Thecc.09G061900' => 'tca', 'Thecc.09G080200' => 'tca', 'Thecc.09G080400' => 'tca', 'Thhalv10017144m.g' => 'esa', 'Thhalv10017148m.g' => 'esa', 'TPR.G24007' => 'tpr', 'TPR.G26289' => 'tpr', 'TWI34G1238' => 'twi', 'TWI34G1506' => 'twi', 'TWI63G0211' => 'twi', 'unitig_578.g16410' => 'ugi', 'unitig_8.g3528' => 'ugi', 'unitig_8.g4686' => 'ugi', 'vmacro17182' => 'vma', 'vmacro19551' => 'vma', 'vmacro23529' => 'vma', 'VMungo0464G1408' => 'vmu', 'VMungo0464G2187' => 'vmu', 'VMungo0720G1042' => 'vmu', 'Zm00001eb172130' => 'zma', 'Zm00001eb327250' => 'zma', 'Zm00001eb415410' => 'zma' ) $gf_id = 'HOM05D001583' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001583' ) $data_identifier = 'HOM05D001583' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 18, 'bol' => (int) 12, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 8, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415410' $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